Micro-computed tomography-current status and developments

Technical note: Micro-computed tomography calibration using dental tissue for bone mineral research

Computed tomography (CT) and microcomputed tomography (μCT) require calibration against density phantoms scanned with specimens or during routine internal calibration for assessment of mineral concentration (MC) and density. In clinical studies involving bone, alternative calibration methods using bodily tissues and fluids ("phantomless" calibration) have been suggested. However, such tissues are seldom available in archeological and osteological research. This study investigates the potential of dental tissue as internal reference for calibration of μCT scans, facilitating the analysis of bone MC. We analyzed 70 molars from 24 extant primate species, including eight human teeth, each scanned with density phantoms for calibration. Our findings indicate that sampling specific regions of molars (lateral aspects of the mesial cusps) yields low variation in enamel and dentine MC values, averaging 1.27 g/cm3 (±0.03) for dentine and 2.25 g/cm3 (±0.03) for enamel. No significant differences were observed across molar types or among scanning procedures, including scanner model, resolution, and filters. An ad hoc test on 12 mandibles revealed low variance in MC between the conventional phantom and dental tissue calibration methods; all 36 measurements (low, medium, and high MC for each mandible) were within 0.05 g/cm3 of each other -81% were within 0.03 g/cm3 and 94% within 0.04 g/cm3. Based on these results, we propose a new "phantomless" calibration technique using these mean enamel and dentine MC values. The presented phantomless calibration method could aid in the assessment of bone pathology and enhance the scope of studies investigating bone structure and physical property variations in archeological, osteological, and laboratory-based research.

Analysis of 3D pathology samples using weakly supervised AI

Human tissue, which is inherently three-dimensional (3D), is traditionally examined through standard-of-care histopathology as limited two-dimensional (2D) cross-sections that can insufficiently represent the tissue due to sampling bias. To holistically characterize histomorphology, 3D imaging modalities have been developed, but clinical translation is hampered by complex manual evaluation and lack of computational platforms to distill clinical insights from large, high-resolution datasets. We present TriPath, a deep-learning platform for processing tissue volumes and efficiently predicting clinical outcomes based on 3D morphological features. Recurrence risk-stratification models were trained on prostate cancer specimens imaged with open-top light-sheet microscopy or microcomputed tomography. By comprehensively capturing 3D morphologies, 3D volume-based prognostication achieves superior performance to traditional 2D slice-based approaches, including clinical/histopathological baselines from six certified genitourinary pathologists. Incorporating greater tissue volume improves prognostic performance and mitigates risk prediction variability from sampling bias, further emphasizing the value of capturing larger extents of heterogeneous morphology.

Sparse2Noise: Low-dose synchrotron X-ray tomography without high-quality reference data

BACKGROUND

Synchrotron radiation computed tomography (SR-CT) holds promise for high-resolution in vivo imaging. Notably, the reconstruction of SR-CT images necessitates a large set of data to be captured with sufficient photons from multiple angles, resulting in high radiation dose received by the object. Reducing the number of projections and/or photon flux is a straightforward means to lessen the radiation dose, however, compromises data completeness, thus introducing noises and artifacts. Deep learning (DL)-based supervised methods effectively denoise and remove artifacts, but they heavily depend on high-quality paired data acquired at high doses. Although algorithms exist for training without high-quality references, they struggle to effectively eliminate persistent artifacts present in real-world data.

METHODS

This work presents a novel low-dose imaging strategy namely Sparse2Noise, which combines the reconstruction data from paired sparse-view CT scan (normal-flux) and full-view CT scan (low-flux) using a convolutional neural network (CNN). Sparse2Noise does not require high-quality reconstructed data as references and allows for fresh training on data with very small size. Sparse2Noise was evaluated by both simulated and experimental data.

RESULTS

Sparse2Noise effectively reduces noise and ring artifacts while maintaining high image quality, outperforming state-of-the-art image denoising methods at same dose levels. Furthermore, Sparse2Noise produces impressive high image quality for ex vivo rat hindlimb imaging with the acceptable low radiation dose (i.e., 0.5 Gy with the isotropic voxel size of 26 μm).

CONCLUSIONS

This work represents a significant advance towards in vivo SR-CT imaging. It is noteworthy that Sparse2Noise can also be used for denoising in conventional CT and/or phase-contrast CT.

Characterization of Biocompatibility of Functional Bioinks for 3D Bioprinting

Three-dimensional (3D) bioprinting with suitable bioinks has become a critical tool for fabricating 3D biomimetic complex structures mimicking physiological functions. While enormous efforts have been devoted to developing functional bioinks for 3D bioprinting, widely accepted bioinks have not yet been developed because they have to fulfill stringent requirements such as biocompatibility and printability simultaneously. To further advance our knowledge of the biocompatibility of bioinks, this review presents the evolving concept of the biocompatibility of bioinks and standardization efforts for biocompatibility characterization. This work also briefly reviews recent methodological advances in image analyses to characterize the biocompatibility of bioinks with regard to cell viability and cell-material interactions within 3D constructs. Finally, this review highlights a number of updated contemporary characterization technologies and future perspectives to further advance our understanding of the biocompatibility of functional bioinks for successful 3D bioprinting.

Mouse embryo phenotyping using X-ray microCT

Microscopic X-ray computed tomography (microCT) is a structural ex vivo imaging technique providing genuine isotropic 3D images from biological samples at micron resolution. MicroCT imaging is non-destructive and combines well with other modalities such as light and electron microscopy in correlative imaging workflows. Protocols for staining embryos with X-ray dense contrast agents enable the acquisition of high-contrast and high-resolution datasets of whole embryos and specific organ systems. High sample throughput is achieved with dedicated setups. Consequently, microCT has gained enormous importance for both qualitative and quantitative phenotyping of mouse development. We here summarize state-of-the-art protocols of sample preparation and imaging procedures, showcase contemporary applications, and discuss possible pitfalls and sources for artefacts. In addition, we give an outlook on phenotyping workflows using microscopic dual energy CT (microDECT) and tissue-specific contrast agents.

An optimized workflow for microCT imaging of formalin‐fixed and paraffin‐embedded ( FFPE ) early equine embryos

Here, we describe a workflow for high‐detail microCT imaging of formalin‐fixed and paraffin‐embedded (FFPE) equine embryos recovered on Day 34 of pregnancy (E34), a period just before placenta formation. The presented imaging methods are suitable for large animals' embryos with intention to study morphological and developmental aspects, but more generally can be adopted for all kinds of FFPE tissue specimens. Microscopic 3D imaging techniques such as microCT are important tools for detecting and studying normal embryogenesis and developmental disorders. To date, microCT imaging of vertebrate embryos was mostly done on embryos that have been stained with an X‐ray dense contrast agent. Here, we describe an alternative imaging procedure that allows to visualize embryo morphology and organ development in unstained FFPE embryos. Two aspects are critical for high‐quality data acquisition: (i) a proper sample mounting leaving as little as possible paraffin around the sample and (ii) an image filtering pipeline that improves signal‐to‐noise ratio in these inherently low‐contrast data sets. The presented workflow allows overview imaging of the whole embryo proper and can be used for determination of organ volumes and development. Furthermore, we show that high‐resolution interior tomographies can provide virtual histology information from selected regions of interest. In addition, we demonstrate that microCT scanned embryos remain intact during the scanning procedure allowing for a subsequent investigation by routine histology and/or immunohistochemistry. This makes the presented workflow applicable also to archival paraffin‐embedded material.

Beyond the behavioural phenotype: Uncovering mechanistic foundations in aquatic eco-neurotoxicology

During the last decade, there has been an increase in awareness of how anthropogenic pollution can alter behavioural traits of diverse aquatic organisms. Apart from understanding profound ecological implications, alterations in neuro-behavioural indices have emerged as sensitive and physiologically integrative endpoints in chemical risk assessment. Accordingly, behavioural ecotoxicology and broader eco-neurotoxicology are becoming increasingly popular fields of research that span a plethora of fundamental laboratory experimentations as well as applied field-based studies. Despite mounting interest in aquatic behavioural ecotoxicology studies, there is, however, a considerable paucity in deciphering the mechanistic foundations underlying behavioural alterations upon exposure to pollutants. The behavioural phenotype is indeed the highest-level integrative neurobiological phenomenon, but at its core lie myriads of intertwined biochemical, cellular, and physiological processes. Therefore, the mechanisms that underlie changes in behavioural phenotypes can stem among others from dysregulation of neurotransmitter pathways, electrical signalling, and cell death of discrete cell populations in the central and peripheral nervous systems. They can, however, also be a result of toxicity to sensory organs and even metabolic dysfunctions. In this critical review, we outline why behavioural phenotyping should be the starting point that leads to actual discovery of fundamental mechanisms underlying actions of neurotoxic and neuromodulating contaminants. We highlight potential applications of the currently existing and emerging neurobiology and neurophysiology analytical strategies that should be embraced and more broadly adopted in behavioural ecotoxicology. Such strategies can provide new mechanistic discoveries instead of only observing the end sum phenotypic effects.

Experimental Study on the Characterization of Orientation of Polyester Short Fibers in Rubber Composites by an X-ray Three-Dimensional Microscope

Polyester-short-fiber-reinforced rubber composites have been detected by an X-ray three-dimensional microscope, and then the three-dimensional reconstruction of the image has been carried out to characterize the orientation of polyester short fibers in the composites for the first time. Based on the summary of three traditional methods and mechanisms of characterizing the orientation of polyester short fibers by the numerical parameter method, the direct test method, and the indirect test method, the method and mechanism of the X-ray three-dimensional microscope applied to the orientation characterization of polyester short fibers have been studied. The combination of the center point and threshold segmentation methods has been used to distinguish which fiber section belongs to the same fiber, and the identification of the whole short fiber in different slice images has been realized for the first time. Moreover, Avizo software has been used to realize the three-dimensional reconstruction of a polyester short fiber scanning image. The obtained data have been integrated and the orientation angle and orientation degree have been quantitatively characterized for the first time. This has filled the key technical problem of quantitative characterization of the orientation angle and orientation degree of polyester fibers. The image has been verified by 3Dmed software, and furthermore, the accuracy of the three-dimensional reconstruction results has been verified.

Ripples at Edges of Blooming Lilies and Torn Plastic Sheets

Ripples arise at edges of petals of blooming Lilium casablanca flowers and at edges of torn plastic sheets. In both systems, ripples are a consequence of excess length along the edge of a sheet. Through the use of time-lapse videos of blooming lilies and published images of torn plastic sheets, we find that ripples in both systems are well-described by the scaling relationship a∝w(L-w), where a is amplitude, w is wavelength, and L is arc length. A phenomenological relationship previously reported for self-similar ripple patterns, namely 〈a〉∝〈w〉, can be recovered by assuming that buckling stress is constant. Excess length along petal edges can also influence their overall Gaussian curvature, such that petals invert from a cup shape to a saddle shape upon blooming. Previous simulations of these shape changes have assumed that petal thickness decreases at least quadratically. Here, we evaluate tomograms of several varieties of lily buds and find that this assumption is valid along the short axis of the buds, but not the long axis. A challenge of employing traditional tomography methods to measure petal thickness is that the sample is destroyed; a single bud cannot be followed through the entire blooming process. To address this challenge, we provide proof of principle that the non-destructive, label-free method of X-ray tomography produces high-contrast 3-dimensional scans on time scales short enough to follow lily blooming.

Co-Clinical Imaging Resource Program (CIRP): Bridging the Translational Divide to Advance Precision Medicine

The National Institutes of Health’s (National Cancer Institute) precision medicine initiative emphasizes the biological and molecular bases for cancer prevention and treatment. Importantly, it addresses the need for consistency in preclinical and clinical research. To overcome the translational gap in cancer treatment and prevention, the cancer research community has been transitioning toward using animal models that more fatefully recapitulate human tumor biology. There is a growing need to develop best practices in translational research, including imaging research, to better inform therapeutic choices and decision-making. Therefore, the National Cancer Institute has recently launched the Co-Clinical Imaging Research Resource Program (CIRP). Its overarching mission is to advance the practice of precision medicine by establishing consensus-based best practices for co-clinical imaging research by developing optimized state-of-the-art translational quantitative imaging methodologies to enable disease detection, risk stratification, and assessment/prediction of response to therapy. In this communication, we discuss our involvement in the CIRP, detailing key considerations including animal model selection, co-clinical study design, need for standardization of co-clinical instruments, and harmonization of preclinical and clinical quantitative imaging pipelines. An underlying emphasis in the program is to develop best practices toward reproducible, repeatable, and precise quantitative imaging biomarkers for use in translational cancer imaging and therapy. We will conclude with our thoughts on informatics needs to enable collaborative and open science research to advance precision medicine.

Intravital Whole-Process Monitoring Thermo-Chemotherapy Via 2D Silicon Nanoplatform: A Macro Guidance and Long-Term Microscopic Precise Imaging Strategy

Tumor angiogenesis is a complex process that is unamenable to intravital whole-process monitoring, especially on microscopic assessment of tumor microvessel and quantifying microvascular hemodynamics before and after the nanotherapeutics, which hinder the understanding of nanotheranostics outcomes in tumor treatment. Herein, a new photoacoustic (PA) imaging-optical coherence tomography angiography (OCTA)-laser speckle (LS) multimodal imaging strategy is first proposed, which is not only able to precisely macro guide the thermo-chemotherapy of tumor by monitoring blood oxygen saturation (SaO2 ) and hemoglobin content (HbT), but also capable of long-term microscopic investigating the microvessel morphology (microvascular density) and hemodynamics changes (relative blood flow) before and after the nanotherapeutics in vivo. Moreover, to realize the tumor thermo-chemotherapy treatment based on this novel multimodal imaging strategy, a 2D 5-fluorouracil silicon nanosheets (5-Fu-Si NSs) therapeutic agent is designed. Furthermore, 2D high-resolution tumor microvascular images in different stage display that tendency of the thermo-chemotherapy effect is closely associated with tumor angiogenesis. Taken together, the investigations establish the fundamental base in theory and technology for further tailoring the novel specific diagnosis and treatment strategy in tumor. More importantly, this technique will be beneficial to evaluate the tumor microvascular response to nanotherapeutics at microscale.

Photopolymerized Porous Hydrogels

Hydrogels are polymeric networks highly swollen with water. Because of their versatility and properties mimicking biological tissues, they are very interesting for biomedical applications. In this aim, the control of porosity is of crucial importance since it governs the transport properties and influences the fate of cells cultured onto or into the hydrogels. Among the techniques allowing for the elaboration of hydrogels, photopolymerization or photo-cross-linking are probably the most powerful and versatile synthetic routes. This Review aims at giving an overview of the literature dealing with photopolymerized hydrogels for which the generation or characterization of porosity is studied. First, the materials (polymers and photoinitiating systems) used for synthesizing hydrogels are presented. The different ways for generating porosity in the photopolymerized hydrogels are explained, and the characterization techniques allowing adequate study of the porosity are presented. Finally, some applications in the field of controlled release and tissue engineering are reviewed.

Guidelines for Micro-Computed Tomography Analysis of Rodent Dentoalveolar Tissues

Micro–computed tomography (μCT) has become essential for analysis of mineralized as well as nonmineralized tissues and is therefore widely applicable in the life sciences. However, lack of standardized approaches and protocols for scanning, analyzing, and reporting data often makes it difficult to understand exactly how analyses were performed, how to interpret results, and if findings can be broadly compared with other models and studies. This problem is compounded in analysis of the dentoalveolar complex by the presence of four distinct mineralized tissues: enamel, dentin, cementum, and alveolar bone. Furthermore, these hard tissues interface with adjacent soft tissues, the dental pulp and periodontal ligament (PDL), making for a complex organ. Drawing on others' and our own experience analyzing rodent dentoalveolar tissues by μCT, we introduce techniques to successfully analyze dentoalveolar tissues with similar or disparate compositions, densities, and morphological characteristics. Our goal is to provide practical guidelines for μCT analysis of rodent dentoalveolar tissues, including approaches to optimize scan parameters (filters, voltage, voxel size, and integration time), reproducibly orient samples, define regions and volumes of interest, segment and subdivide tissues, interpret findings, and report methods and results. We include illustrative examples of analyses performed on genetically engineered mouse models with phenotypes in enamel, dentin, cementum, and alveolar bone. The recommendations are designed to increase transparency and reproducibility, promote best practices, and provide a basic framework to apply μCT analysis to the dentoalveolar complex that can also be extrapolated to a variety of other tissues of the body. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC. on behalf of American Society for Bone and Mineral Research.

The application of micro-CT in egg-laying hen bone analysis: introducing an automated bone separation algorithm

The application of micro-CT in small animal research, especially on bone health, has risen exponentially in recent years. However, its application in egg-laying hen bone analysis was still limited. This review introduces the technical aspects of micro-CT in egg-laying hen bone analysis, especially with the medullary bones presented in the cavity. In order to acquate application of micro-CT for laying hen bone research, image acquisition, reconstruction, and analysis settings need to be adjusted properly. The key difference regarding the application of micro-CT in laying hen bone compared to other small animals such as mice and rats was the larger bone size and more complex structures of medullary and trabecular bones. In order to analyze the details of laying hen bone structures, the volume of interest for laying hen should be selected at a region where all 3 bones are present (critical, trabecular, and medullary bone). Owing to the complexity of bone structures, the conventional techniques are not useful to distinguish the trabecular bone and medullary bone in laying hens accurately. In the current review, an automated segmentation algorithm is described to allow researchers to segment bone compartments without human bias. The algorithm is designed according to the morphology difference of medullary bones compared to trabecular and cortical bones. In this procedure, the loosely woven bones were separated by applying dual thresholds. The medullary calcium chunks were separated by opening or closing procedures, where we defined the diameter of medullary chunks being higher than the trabecular bone thickness as a separation trait. The application of micro-CT in laying hen bone health assessment will significantly expand our understanding of chicken bone physiology and osteoporosis, contributing to improve welfare in laying hens.

Mineralization of Biomaterials for Bone Tissue Engineering

Mineralized biomaterials have been demonstrated to enhance bone regeneration compared to their non-mineralized analogs. As non-mineralized scaffolds do not perform as well as mineralized scaffolds in terms of their mechanical and surface properties, osteoconductivity and osteoinductivity, mineralization strategies are promising methods in the development of functional biomimetic bone scaffolds. In particular, the mineralization of three-dimensional (3D) scaffolds has become a promising approach for guided bone regeneration. In this paper, we review the major approaches used for mineralizing tissue engineering constructs. The resulting scaffolds provide minerals chemically similar to the inorganic component of natural bone, carbonated apatite, Ca5(PO4,CO3)3(OH). In addition, we discuss the characterization techniques that are used to characterize the mineralized scaffolds, such as the degree of mineralization, surface characteristics, mechanical properties of the scaffolds, and the chemical composition of the deposited minerals. In vitro cell culture studies show that the mineralized scaffolds are highly osteoinductive. We also summarize, based on literature examples, the applications of 3D mineralized constructs, as well as the rationale behind their use. The mineralized scaffolds have improved bone regeneration in animal models due to the enhanced mechanical properties and cell recruitment capability making them a preferable option for bone tissue engineering over non-mineralized scaffolds.

Investigation of optimal sample preparation conditions with potassium triiodide and optimal imaging settings for microfocus computed tomography of excised cat hearts

OBJECTIVE

To determine optimal sample preparation conditions with potassium triiodide (I₂KI) and optimal imaging settings for microfocus CT (micro-CT) of excised cat hearts.

SAMPLE

7 excised hearts (weight range, 10 to 17.6 g) obtained from healthy adult cats after euthanasia by IV injection of pentobarbital sodium.

PROCEDURES

Following excision, the hearts were preserved in 10% formaldehyde solution. Six hearts were immersed in 1.25% I₂KI solution (n = 3) or 2.5% I₂KI solution (3) for a 12-day period. Micro-CT images were acquired at time 0 (prior to iodination) then approximately every 24 and 48 hours thereafter to determine optimal sample preparation conditions (ie, immersion time and concentration of I₂KI solution). Identified optimal conditions were then used to prepare the seventh heart for imaging; changes in voltage, current, exposure time, and gain on image quality were evaluated to determine optimal settings (ie, maximal signal-to-noise and contrast-to-noise ratios). Images were obtained at a voxel resolution of 30 μm. A detailed morphological assessment of the main cardiac structures of the seventh heart was then performed.

RESULTS

Immersion in 2.5% I₂KI solution for 48 hours was optimal for sample preparation. The optimal imaging conditions included a tube voltage of 100 kV, current of 150 μA, and exposure time of 354 milliseconds; scan duration was 12 minutes.

CONCLUSIONS AND CLINICAL RELEVANCE

Results provided an optimal micro-CT imaging protocol for excised cat hearts prepared with I₂KI solution that could serve as a basis for future studies of micro-CT for high resolution 3-D imaging of cat hearts.

Three dimensional (3D) imaging techniques in orthodontics-An update

3D imaging is a technique which develops or creates the impression of depth within an image by deploying 2D data into 3-dimensional format. To aid in quality regulating processes for industrial purposes, 3D imaging has become an extremely valuable factor. Owing to their various drawbacks, a wide range of investigative methods formulated for demonstration of facial structures and the dentition were dilapidated. Currently in medicine, the most prevalent method is perhaps 3D imaging technique renders thorough and problem specific information regarding hard and the soft tissues, such as Computerized Tomography (CT), Cone Beam Computerized Tomography (CBCT), Micro Computerized Tomography (MCT), 3D laser scanning, structured light technique, stereophotogrammetry or 3D surface imaging systems (3dMD), 3D facial morphometry (3DFM), Tuned Aperture Computed Tomography (TACT), and Magnetic Resonance Imaging (MRI). 3D imaging techniques in orthodontics plays an important role by facilitating more elaborated diagnostic information on the precise cases like patients having craniofacial anomalies. Hence, the aim of this study was to review advances in 3D imaging with in the field of orthodontics.

The Opportunities and Use of Imaging to Measure Target Engagement

Lack of efficacy and poor safety outcomes are deemed to be the greatest causes of clinical failure of novel therapeutics. The use of biomarkers that give accurate information on target engagement, providing confidence that pharmacological activity in the target organ is being achieved, is key in optimizing clinical success. Without a measurement of target engagement, it can be very difficult to discern the basis for any lack of efficacy of a drug molecule within the pharmaceutical industry. Target engagement can be measured in both an in vitro and in vivo setting, and in recent years imaging measurements have been used frequently in drug discovery and development to assess target engagement and receptor occupancy in both human and animal models. From this perspective, we assess and look at the advancements in both in vivo and ex vivo imaging to demonstrate the enormous potential that imaging has as an application to provide a greater understanding of target engagement with a correlative therapeutic impact.

X-ray Micro-Computed Tomography for Nondestructive Three-Dimensional (3D) X-ray Histology

Historically, micro-computed tomography (μCT) has been considered unsuitable for histologic analysis of unstained formalin-fixed, paraffin-embedded soft tissue biopsy specimens because of a lack of image contrast between the tissue and the paraffin. However, we recently demonstrated that μCT can successfully resolve microstructural detail in routinely prepared tissue specimens. Herein, we illustrate how μCT imaging of standard formalin-fixed, paraffin-embedded biopsy specimens can be seamlessly integrated into conventional histology workflows, enabling nondestructive three-dimensional (3D) X-ray histology, the use and benefits of which we showcase for the exemplar of human lung biopsy specimens. This technology advancement was achieved through manufacturing a first-of-kind μCT scanner for X-ray histology and developing optimized imaging protocols, which do not require any additional sample preparation. 3D X-ray histology allows for nondestructive 3D imaging of tissue microstructure, resolving structural connectivity and heterogeneity of complex tissue networks, such as the vascular network or the respiratory tract. We also demonstrate that 3D X-ray histology can yield consistent and reproducible image quality, enabling quantitative assessment of a tissue's 3D microstructures, which is inaccessible to conventional two-dimensional histology. Being nondestructive, the technique does not interfere with histology workflows, permitting subsequent tissue characterization by means of conventional light microscopy-based histology, immunohistochemistry, and immunofluorescence. 3D X-ray histology can be readily applied to a plethora of archival materials, yielding unprecedented opportunities in diagnosis and research of disease.

Numerical simulation of novel concept 4D cardiac microtomography for small rodents based on all-optical Thomson scattering X-ray sources

Accurate dynamic three-dimensional (4D) imaging of the heart of small rodents is required for the preclinical study of cardiac biomechanics and their modification under pathological conditions, but technological challenges are met in laboratory practice due to the very small size and high pulse rate of the heart of mice and rats as compared to humans. In 4D X-ray microtomography (4D μCT), the achievable spatio-temporal resolution is hampered by limitations in conventional X-ray sources and detectors. Here, we propose a proof-of-principle 4D μCT platform, exploiting the unique spatial and temporal features of novel concept, all-optical X-ray sources based on Thomson scattering (TS). The main spatial and spectral properties of the photon source are investigated using a TS simulation code. The entire data acquisition workflow has been also simulated, using a novel 4D numerical phantom of a mouse chest with realistic intra- and inter-cycle motion. The image quality of a typical single 3D time frame has been studied using Monte Carlo simulations, taking into account the effects of the typical structure of the TS X-ray beam. Finally, we discuss the perspectives and shortcomings of the proposed platform.

Cochlear pharmacokinetics - Micro-computed tomography and learning-prediction modeling for transport parameter determination

Inner ear disorders such as sensorineural deafness and genetic diseases may one day be treated with local drug delivery to the inner ear. Current pharmacokinetic models have been based on invasive methods to measure drug concentrations, limiting them in spatial resolution, and restricting the research to larger rodents. We developed an intracochlear pharmacokinetic model based on an imaging, learning-prediction (LP) paradigm for learning transport parameters in the murine cochlea. This was achieved using noninvasive micro-computed tomography imaging of the cochlea during in vivo infusion of a contrast agent at the basal end of scala tympani through a cochleostomy. Each scan was registered in 3-D to a cochlear atlas to segment the cochlear regions with high accuracy, enabling concentrations to be extracted along the length of each scala. These spatio-temporal concentration profiles were used to learn a concentration dependent diffusion coefficient, and transport parameters between the major scalae and to clearance. The LP model results are comparable to the current state of the art model, and can simulate concentrations for cases involving different infusion molecules and different drug delivery protocols. Forward simulation results with pulsatile delivery suggest the pharmacokinetic model can be used to optimize drug delivery protocols to reduce total drug delivered and the potential for toxic side effects. While developed in the challenging murine cochlea, the processes are scalable to larger animals and different drug infusion paradigms.

A Computed Tomographic and Pathological Study of Equine Cheek Teeth Infundibulae Extracted From Asymptomatic Horses. Part 2: MicroCT, Gross, and Histological Findings

Background: Equine maxillary cheek teeth infundibulae are frequently affected by developmental and acquired disorders, but the imaging, gross, and histological features of normal and abnormal infundibulae remain incompletely understood. Objective: To perform MicroCT, gross examination, and histology on sectioned teeth and compare the imaging and anatomical findings. Study design: Ex vivo original study. Methods: Eight maxillary cheek teeth of different ages and with varying grades of unilateral (n = 5) or bilateral (n = 3) occlusal infundibular caries were extracted from equine heads obtained from an abattoir. The teeth were imaged by MicroCT, then transversely sectioned and grossly and histologically examined, with the imaging and gross and histological anatomical findings examined and compared. Results: Fifteen infundibulae, including two without occlusal caries had subocclusal cemental hypoplasia or caries. One infundibulum without occlusal caries had no subocclusal cemental defects. Histologically, hypoplastic cemental areas consisted of irregularly-shaped, wide central channels, with multiple, large, cylindrical side-branches that extended peripherally to a variable extent. Cementum with extensive, wide, empty channels, and cementum with a more irregular moth-eaten appearance had dark or eroded gross appearance and a low HU on CT. Some infundibulae had cement-free areas that only contained fragments of collagen-like material, especially at their apical aspects (apical cemental hypoplasia). Carious subocclusal areas had connections with the occlusal surface and had disrupted cemental architecture, including of their central vascular channel that, along with their side branches, contained degraded food, and cemental debris. Main Limitations: No clinical histories or accurate ages were available for these eight teeth. Conclusions: Hypoplastic cemental lesions, including at central linear and apical sites, histologically contain areas with multiple wide-branched, cylindrical channels or even areas of total cement hypoplasia visible on gross sections When such cemental defects contact the occlusal surface due to normal wear, food impaction, and caries can ensue.

Micro-CT myelography using contrast-enhanced digital subtraction: feasibility and initial results in healthy rats

PURPOSE

The spinal subarachnoid space (SSAS) is vital for neural performance. Although models of spinal diseases and trauma are used frequently, no methods exist to obtain high-resolution myelograms in rodents. Thereby, our aim was to explore the feasibility of obtaining high-resolution micro-CT myelograms of rats by contrast-enhanced dual-energy (DE) and single-energy (SE) digital subtraction.

METHODS

Micro-CT contrast-enhanced DE and SE imaging protocols were implemented with live adult rats (total of 18 animals). For each protocol, contrast agents based on iodine (Iomeron® 400 and Fenestra® VC) and gold nanoparticles (AuroVist™ 15 nm) were tested. For DE, images at low- and high-energy settings were acquired after contrast injection; for SE, one image was acquired before and the other after contrast injection. Post-processing consisted of region of interest selection, image registration, weighted subtraction, and longitudinal alignment.

RESULTS

High-resolution myelograms were obtained with contrast-enhanced digital subtraction protocols. After qualitative and quantitative (contrast-to-noise ratio) analyses, we found that the SE acquisition protocol with Iomeron® 400 provides the best images. 3D contour renderings allowed visualization of SSAS and identification of some anatomical structures within it.

CONCLUSION

This in vivo study shows the potential of SE contrast-enhanced myelography for imaging SSAS in rat. This approach yields high-resolution 3D images without interference from adjacent anatomical structures, providing an innovative tool for further assessment of studies involving rat SSAS.

Evaluation of maxillary trabecular microstructure as an indicator of implant stability by using 2 cone beam computed tomography systems and micro-computed tomography

OBJECTIVE

The aim of this study was to assess the trabecular microarchitecture of the maxilla by using cone beam computed tomography (CBCT) and micro-computed tomography (micro-CT) ex vivo.

STUDY DESIGN

Seventeen maxillary cadaver specimens were scanned by using micro-CT and CBCT devices. Samples were scanned with 2 CBCT devices at different voxel sizes (0.08, 0.125, and 0.160 mm for 3-D Accuitomo 170; 0.75 and 0.200 mm for Planmeca Promax 3-D Max). Morphometric parameters, such as bone volume/total volume (BV/TV) ratio, trabecular thickness (Tb.Th), trabecular separation (Tb.Sp), trabecular number (Tb.N), and degree of anisotropy (DA) were assessed by using CTAnalyzer software. Bland-Altman limits of agreement and intraclass correlation coefficient (ICC) were performed to evaluate agreement between CBCT and micro-CT in consideration of measured morphometric parameters. Statistical significance was set at P < .05.

RESULTS

The BV/TV, Tb.Th, Tb.Sp, and DA values were higher for CBCT images compared with micro-CT images, whereas the Tb.N value was lower with CBCT images than with micro-CT images. The BV/TV and DA parameters showed the highest agreement between CBCT and micro-CT devices (ICC = 0.421 for BV/TV and ICC = 0.439 for DA; P < .01).

CONCLUSIONS

The BV/TV and DA parameters measured on CBCT obtained at the smallest voxel size were found to be useful for the assessment of maxillary trabecular microstructure.

Micro-CT - a digital 3D microstructural voyage into scaffolds: a systematic review of the reported methods and results

BACKGROUND

Cell behavior is the key to tissue regeneration. Given the fact that most of the cells used in tissue engineering are anchorage-dependent, their behavior including adhesion, growth, migration, matrix synthesis, and differentiation is related to the design of the scaffolds. Thus, characterization of the scaffolds is highly required. Micro-computed tomography (micro-CT) provides a powerful platform to analyze, visualize, and explore any portion of interest in the scaffold in a 3D fashion without cutting or destroying it with the benefit of almost no sample preparation need.

MAIN BODY

This review highlights the relationship between the scaffold microstructure and cell behavior, and provides the basics of the micro-CT method. In this work, we also analyzed the original papers that were published in 2016 through a systematic search to address the need for specific improvements in the methods section of the papers including the amount of provided information from the obtained results.

CONCLUSION

Micro-CT offers a unique microstructural analysis of biomaterials, notwithstanding the associated challenges and limitations. Future studies that will include micro-CT characterization of scaffolds should report the important details of the method, and the derived quantitative and qualitative information can be maximized.

Dual-energy computed tomography using a gantry-based preclinical cone-beam microcomputed tomography scanner

Dual-energy microcomputed tomography (DECT) can provide quantitative information about specific materials of interest, facilitating automated segmentation, and visualization of complex three-dimensional tissues. It is possible to implement DECT on currently available preclinical gantry-based cone-beam micro-CT scanners; however, optimal decomposition image quality requires customized spectral shaping (through added filtration), optimized acquisition protocols, and elimination of misregistration artifacts. We present a method for the fabrication of customized x-ray filters-in both shape and elemental composition-needed for spectral shaping. Fiducial markers, integrated within the sample holder, were used to ensure accurate co-registration between sequential low- and high-energy image volumes. The entire acquisition process was automated through the use of a motorized filter-exchange mechanism. We describe the design, implementation, and evaluation of a DECT system on a gantry-based-preclinical cone-beam micro-CT scanner.

Effectiveness of the Multilayered Caries Model and Visuo-tactile Virtual Reality Simulator for Minimally Invasive Caries Removal: A Randomized Controlled Trial

This work presents the multilayered caries model with a visuo-tactile virtual reality simulator and a randomized controlled trial protocol to determine the effectiveness of the simulator in training for minimally invasive caries removal. A three-dimensional, multilayered caries model was reconstructed from 10 micro-computed tomography (CT) images of deeply carious extracted human teeth before and after caries removal. The full grey scale 0-255 yielded a median grey scale value of 0-9, 10-18, 19-25, 26-52, and 53-80 regarding dental pulp, infected carious dentin, affected carious dentin, normal dentin, and normal enamel, respectively. The simulator was connected to two haptic devices for a handpiece and mouth mirror. The visuo-tactile feedback during the operation varied depending on the grey scale. Sixth-year dental students underwent a pretraining assessment of caries removal on extracted teeth. The students were then randomly assigned to train on either the simulator (n=16) or conventional extracted teeth (n=16) for 3 days, after which the assessment was repeated. The posttraining performance of caries removal improved compared with pretraining in both groups (Wilcoxon, p&lt;0.05). The equivalence test for proportional differences (two 1-sided t-tests) with a 0.2 margin confirmed that the participants in both groups had identical posttraining performance scores (95% CI=0.92, 1; p=0.00). In conclusion, training on the micro-CT multilayered caries model with the visuo-tactile virtual reality simulator and conventional extracted tooth had equivalent effects on improving performance of minimally invasive caries removal.

[Establishment of micro-vessels model of cross-boundary perforator flap in rat via digital technology]

Objective

To investigate the feasibility and application value of digital technology in establishing the micro-vessels model of cross-boundary perforator flap in rat.

Methods

Twenty 8-week-old female Sprague Dawley rats, weighing 280-300 g, were used to established micro-vessels model. The cross-boundary perforator flaps of 10 cm×3 cm in size were prepared at the dorsum of 20 rats; then the flaps were sutured in situ. Ten rats were randomly picked up at 3 and 7 days after operation in order to observe the necrosis of flap and measure the percentage of flap necrosis area; the lead-oxide gelatin solution was used for vessels perfusion; flaps were harvested and three-dimensional reconstruction of micro-vessel was performed after micro-CT scanning. Vascular volume and total length were measured via Matlable 7.0 software.

Results

The percentage of flap necrosis area at 3 days after operation was 19.08%±3.64%, which was significantly lower than that at 7 days (39.76%±3.76%; t=10.361, P=0.029). Three-dimensional reconstruction via the micro-CT clearly showed the morphological alteration of micro-vessel of the flap. At 3 days after operation, the vascular volume of the flap was (1 240.23±89.71) mm ³ and the total length was (245.94±29.38) mm. At 7 days after operation, the vascular volume of the flap was (1 036.96±88.97) mm ³ and the total length was (143.20±30.28) mm. There were significant differences in the vascular volume and the total length between different time points ( t=5.088, P=0.000; t=7.701, P=0.000).

Conclusion

The digital technology can be applied to visually observe and objectively evaluate the morphological alteration of the micro-vessels of the flap, and provide technical support for the study of vascular model of flap.

Neutron tomographic imaging of bone-implant interface: Comparison with X-ray tomography

Metal implants, in e.g. joint replacements, are generally considered to be a success. As mechanical stability is important for the longevity of a prosthesis, the biological reaction of the bone to the mechanical loading conditions after implantation and during remodelling determines its fate. The bone reaction at the implant interface can be studied using high-resolution imaging. However, commonly used X-ray imaging suffers from image artefacts in the close proximity of metal implants, which limit the possibility to closely examine the bone at the bone-implant interface. An alternative ex vivo 3D imaging method is offered by neutron tomography. Neutrons interact with matter differently than X-rays; therefore, this study explores if neutron tomography may be used to enrich studies on bone-implant interfaces. A stainless steel screw was implanted in a rat tibia and left to integrate for 6weeks. After extracting the tibia, the bone-screw construct was imaged using X-ray and neutron tomography at different resolutions. Artefacts were visible in all X-ray images in the close proximity of the implant, which limited the ability to accurately quantify the bone around the implant. In contrast, neutron images were free of metal artefacts, enabling full analysis of the bone-implant interface. Trabecular structural bone parameters were quantified in the metaphyseal bone away from the implant using all imaging modalities. The structural bone parameters were similar for all images except for the lowest resolution neutron images. This study presents the first proof-of-concept that neutron tomographic imaging can be used for ex-vivo evaluation of bone microstructure and that it constitutes a viable, new tool to study the bone-implant interface tissue remodelling.

Micro-computed tomography characterization of tissue engineering scaffolds: effects of pixel size and rotation step

Quantitative assessment of micro-structure of materials is of key importance in many fields including tissue engineering, biology, and dentistry. Micro-computed tomography (µ-CT) is an intensively used non-destructive technique. However, the acquisition parameters such as pixel size and rotation step may have significant effects on the obtained results. In this study, a set of tissue engineering scaffolds including examples of natural and synthetic polymers, and ceramics were analyzed. We comprehensively compared the quantitative results of µ-CT characterization using 15 acquisition scenarios that differ in the combination of the pixel size and rotation step. The results showed that the acquisition parameters could statistically significantly affect the quantified mean porosity, mean pore size, and mean wall thickness of the scaffolds. The effects are also practically important since the differences can be as high as 24% regarding the mean porosity in average, and 19.5 h and 166 GB regarding the characterization time and data storage per sample with a relatively small volume. This study showed in a quantitative manner the effects of such a wide range of acquisition scenarios on the final data, as well as the characterization time and data storage per sample. Herein, a clear picture of the effects of the pixel size and rotation step on the results is provided which can notably be useful to refine the practice of µ-CT characterization of scaffolds and economize the related resources.

Early clinical applications for imaging at microscopic detail: microfocus computed tomography (micro-CT)

Microfocus CT (micro-CT) has traditionally been used in industry and preclinical studies, although it may find new applicability in the routine clinical setting. It can provide high-resolution three-dimensional digital imaging data sets to the same level of detail as microscopic examination without the need for tissue dissection. Micro-CT is already enabling non-invasive detailed internal assessment of various tissue specimens, particularly in breast imaging and early gestational fetal autopsy, not previously possible from more conventional modalities such as MRI or CT. In this review, we discuss the technical aspects behind micro-CT image acquisition, how early work with small animal studies have informed our knowledge of human disease and the imaging performed so far on human tissue specimens. We conclude with potential future clinical applications of this novel and emerging technique.

Experimentally reducing corticosterone mitigates rapid captivity effects on behavior, but not body composition, in a wild bird

Wild animals and captives display physiological and behavioral differences, and it has been hypothesized, but rarely tested, that these differences are caused by sustained elevation of the hormone corticosterone. We used repeated computed tomography (CT) imaging to examine body composition changes in breeding male and female wild house sparrows (Passer domesticus; n=20) in response to two weeks of captivity, and assessed behavioral changes using video recordings. Half of the birds received the drug mitotane, which significantly decreased stress-induced corticosterone titers compared to controls. Based on the CT images, fat volumes increased, and pectoralis muscle density and heart and testes volumes decreased, over the two weeks of captivity in both groups of birds. However, beak-wiping, a behavior that can indicate anxiety and aggression, showed increased occurrence in controls compared to mitotane-treated birds. While our results do not support the hypothesis that these body composition changes were primarily driven by stress-induced corticosterone, our data suggest that experimentally reducing stress-induced corticosterone may mitigate some captivity-induced behavioral changes. Broadly, our results emphasize that researchers should take behavioral and physiological differences between free-living animals and captives into consideration when designing studies and interpreting results. Further, time in captivity should be minimized when birds will be reintroduced back to the wild.

Rotary shear experiments under X-ray micro-computed tomography

A rotary shear apparatus (ERDμ-T) was designed, assembled, and calibrated to study frictional behavior. We paired the apparatus with X-ray micro-computed tomography (μCT) to inspect in situ and in operando deformation of the tested specimen. This technology allows us to observe how two rough surfaces interact and deform without perturbing the experimental conditions (e.g., pressure, temperature, and sample position). We performed an experiment employing an aluminum alloy sample to demonstrate the capability of the apparatus. The sample was sheared at incremental steps, and during shearing, normal force, sample shortening, torque, and shearing velocity were measured. The measurements were associated to the μCT imagery, giving a comprehensive understanding of the deformation processes of the samples. The present contribution demonstrates that the ERDμ-T allows (1) linking the variation of physical parameters to the evolution of internal structures of the sample and (2) shedding light on fracturing and frictional sliding processes in solid materials.

Imaging of Orthotopic Glioblastoma Xenografts in Mice Using a Clinical CT Scanner: Comparison with Micro-CT and Histology

Purpose

There is an increasing need for small animal in vivo imaging in murine orthotopic glioma models. Because dedicated small animal scanners are not available ubiquitously, the applicability of a clinical CT scanner for visualization and measurement of intracerebrally growing glioma xenografts in living mice was validated.

Materials and Methods

2.5x10⁶ U87MG cells were orthotopically implanted in NOD/SCID/ᵞc^-/- mice (n = 9). Mice underwent contrast-enhanced (300 μl Iomeprol i.v.) imaging using a micro-CT (80 kV, 75 μAs, 360° rotation, 1,000 projections, scan time 33 s, resolution 40 x 40 x 53 μm) and a clinical CT scanner (4-row multislice detector; 120 kV, 150 mAs, slice thickness 0.5 mm, feed rotation 0.5 mm, resolution 98 x 98 x 500 μm). Mice were sacrificed and the brain was worked up histologically. In all modalities tumor volume was measured by two independent readers. Contrast-to-noise ratio (CNR) and Signal-to-noise ratio (SNR) were measured from reconstructed CT-scans (0.5 mm slice thickness; n = 18).

Results

Tumor volumes (mean±SD mm³) were similar between both CT-modalities (micro-CT: 19.8±19.0, clinical CT: 19.8±18.8; Wilcoxon signed-rank test p = 0.813). Moreover, between reader analyses for each modality showed excellent agreement as demonstrated by correlation analysis (Spearman-Rho >0.9; p<0.01 for all correlations). Histologically measured tumor volumes (11.0±11.2) were significantly smaller due to shrinkage artifacts (p<0.05). CNR and SNR were 2.1±1.0 and 1.1±0.04 for micro-CT and 23.1±24.0 and 1.9±0.7 for the clinical CTscanner, respectively.

Conclusion

Clinical CT scanners may reliably be used for in vivo imaging and volumetric analysis of brain tumor growth in mice.

Synchrotron Imaging Assessment of Bone Quality

Bone is a complex hierarchical structure, and its principal function is to resist mechanical forces and fracture. Bone strength depends not only on the quantity of bone tissue but also on the shape and hierarchical structure. The hierarchical levels are interrelated, especially the micro-architecture, collagen and mineral components; hence, analysis of their specific roles in bone strength and stiffness is difficult. Synchrotron imaging technologies including micro-CT and small/wide angle X-ray scattering/diffraction are becoming increasingly popular for studying bone because the images can resolve deformations in the micro-architecture and collagen-mineral matrix under in situ mechanical loading. Synchrotron cannot be directly applied in vivo due to the high radiation dose but will allow researchers to carry out systematic multifaceted studies of bone ex vivo. Identifying characteristics of aging and disease will underpin future efforts to generate novel devices and interventional therapies for assessing and promoting healthy aging. With our own research work as examples, this paper introduces how synchrotron imaging technology can be used with in situ testing in bone research.

A novel design of ultrafast micro-CT system based on carbon nanotube: A feasibility study in phantom

Artifacts induced by respiratory motion during routine diagnosis severely degrades the image quality. The increase of scanning speed plays an important role to avoid motion artifacts. Limited to the mechanical structure of conventional CT, the increase of gantry rotational speed is unsustainable and a more feasible way is to increase the number of X-ray sources and detectors like the dual-source CT. This paper focuses on high-speed scanning CT and proposes a novel ultrafast micro-CT (UMCT) system based on carbon nanotube (CNT). At each exposure position, all of the X-ray sources are fast activated by turns and the flat-panel detectors collect the corresponding projection data. Then, the gantry will be contrarotated 40° to prepare for the next exposure until the rotation covers full 360°. Because each exposure is very fast, the organ motions of in vivo human body can be greatly reduced. This paper introduces the UMCT system design, image reconstruction algorithm and experimental results. Simulation experiment was also carried out on UMCT system. The result validated the feasibility of the UMCT system.

Optical coherence tomography for embryonic imaging: a review

Embryogenesis is a highly complex and dynamic process, and its visualization is crucial for understanding basic physiological processes during development and for identifying and assessing possible defects, malformations, and diseases. While traditional imaging modalities, such as ultrasound biomicroscopy, micro-magnetic resonance imaging, and micro-computed tomography, have long been adapted for embryonic imaging, these techniques generally have limitations in their speed, spatial resolution, and contrast to capture processes such as cardiodynamics during embryogenesis. Optical coherence tomography (OCT) is a noninvasive imaging modality with micrometer-scale spatial resolution and imaging depth up to a few millimeters in tissue. OCT has bridged the gap between ultrahigh resolution imaging techniques with limited imaging depth like confocal microscopy and modalities, such as ultrasound sonography, which have deeper penetration but poorer spatial resolution. Moreover, the noninvasive nature of OCT has enabled live imaging of embryos without any external contrast agents. We review how OCT has been utilized to study developing embryos and also discuss advances in techniques used in conjunction with OCT to understand embryonic development.

Fourier Analysis of Noise Characteristics in Cone-Beam Microtomography Laboratory Scanners

GOAL

We investigate the signal and noise performance of an x-ray microtomography system that incorporates a complementary metal-oxide-semiconductor flat-panel detector as a projection image receptor.

METHODS

Signal and noise performance is analyzed in the Fourier domain using modulation-transfer function (MTF), noise-power spectrum (NPS), and noise-equivalent number of quanta (NEQ) with respect to magnification and different convolution kernels for image reconstruction.

RESULTS

Higher magnification provides lower NPS, and thus, higher NEQ performance in the transaxial planes from microtomography. A window function capable of smoothing the ramp filter edge to below one-half of the Nyquist limit results in better performance in terms of NPS and NEQ. The characteristics of convolution kernels do not affect signal and noise performance in longitudinal planes; hence, MTF performance mainly dominates the NEQ performance. The signal and noise performances investigated in this study are demonstrated with images obtained from the contrast phantom and postmortem mouse.

CONCLUSION

The results of our study could be helpful in developing x-ray microtomography systems based on flat-panel detectors.